Effort versus Reward: Preparing Samples for Fungal Community Characterization in High-Throughput Sequencing Surveys of Soils

Development of an Efficient Fungal DNA Extraction Method To Be Used in Random Amplified Polymorphic DNA–PCR Analysis To Differentiate Cyclopiazonic Acid Mold Producers

(2016) BEATRIZ SÁNCHEZ et al.   JOURNAL OF FOOD PROTECTION

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Quantitative methods for assessment of the impact of different crops on the inoculum density of Rhizoctonia solani AG2-2IIIB in soil

(2014) Barbara Boine et al.   EUROPEAN JOURNAL OF PLANT PATHOLOGY

Parsing ecological signal from noise in next generation amplicon sequencing

(2014) Nhu H. Nguyen et al.   NEW PHYTOLOGIST

Sequence Depth, Not PCR Replication, Improves Ecological Inference from Next Generation DNA Sequencing

(2014) Dylan P. Smith et al.   PLoS One

Enzymatic Treatment of Specimens before DNA Extraction Directly Influences Molecular Detection of Infectious Agents

(2014) Pablo Goldschmidt et al.   PLoS One

Endemism and functional convergence across the North American soil mycobiome

(2014) J. M. Talbot et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Soil biodiversity and soil community composition determine ecosystem multifunctionality

(2014) C. Wagg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Commercial DNA extraction kits impact observed microbial community composition in permafrost samples

(2013) Tatiana A. Vishnivetskaya et al.   FEMS MICROBIOLOGY ECOLOGY

Towards a unified paradigm for sequence-based identification of fungi

(2013) Urmas Kõljalg et al.   MOLECULAR ECOLOGY

Fungal community analysis by high-throughput sequencing of amplified markers - a user's guide

(2013) Björn D. Lindahl et al.   NEW PHYTOLOGIST

Digging the New York City Skyline: Soil Fungal Communities in Green Roofs and City Parks

(2013) Krista L. McGuire et al.   PLoS One

Fungi at a Small Scale: Spatial Zonation of Fungal Assemblages around Single Trees

(2013) Sara Branco et al.   PLoS One

Ion Torrent PGM as Tool for Fungal Community Analysis: A Case Study of Endophytes in Eucalyptus grandis Reveals High Taxonomic Diversity

(2013) Martin Kemler et al.   PLoS One

Abiotic drivers and plant traits explain landscape-scale patterns in soil microbial communities

(2012) Franciska T. de Vries et al.   ECOLOGY LETTERS

A new large scale soil DNA extraction procedure and real-time PCR assay for the detection of Sclerotium cepivorum in soil

(2012) James W. Woodhall et al.   EUROPEAN JOURNAL OF PLANT PATHOLOGY

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Unlocking the potential of metagenomics through replicated experimental design

(2012) Rob Knight et al.   NATURE BIOTECHNOLOGY

Testing the Limits of 454 Pyrotag Sequencing: Reproducibility, Quantitative Assessment and Comparison to T-RFLP Fingerprinting of Aquifer Microbes

(2012) Giovanni Pilloni et al.   PLoS One

Elevated CO2 stimulates grassland soil respiration by increasing carbon inputs rather than by enhancing soil moisture

(2011) E. Carol Adair et al.   GLOBAL CHANGE BIOLOGY

Soil fungal community structure along a soil health gradient in pea fields examined using deep amplicon sequencing

(2011) Lihui Xu et al.   SOIL BIOLOGY & BIOCHEMISTRY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases

(2010) Eva Bellemain et al.   BMC MICROBIOLOGY

Effects of polymerase, template dilution and cycle number on PCR based 16 S rRNA diversity analysis using the deep sequencing method

(2010) Jin-Ya Wu et al.   BMC MICROBIOLOGY

Massively parallel 454-sequencing of fungal communities inQuercusspp. ectomycorrhizas indicates seasonal dynamics in urban and rural sites

(2010) ARI JUMPPONEN et al.   MOLECULAR ECOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Insidious effects of sequencing errors on perceived diversity in molecular surveys

(2010) Ian A. Dickie   NEW PHYTOLOGIST

Co-invasion by Pinus and its mycorrhizal fungi

(2010) Ian A. Dickie et al.   NEW PHYTOLOGIST

454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases

(2010) Leho Tedersoo et al.   NEW PHYTOLOGIST

Direct Detection ofCylindrocarpon destructans, Root Rot Pathogen of Ginseng by Nested PCR from Soil Samples

(2010) Chang Soon Jang et al.   MYCOBIOLOGY

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Innovative Methods for Soil DNA Purification Tested in Soils with Widely Differing Characteristics

(2008) M. Sagova-Mareckova et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems

(2008) Marcel G. A. van der Heijden et al.   ECOLOGY LETTERS

Antagonistic effects of species on C respiration and net N mineralization in soils from mixed coniferous plantations

(2008) Feike A. Dijkstra et al.   FOREST ECOLOGY AND MANAGEMENT

Automated and Manual Methods of DNA Extraction for Aspergillus fumigatus and Rhizopus oryzae Analyzed by Quantitative Real-Time PCR

(2008) A. Francesconi et al.   JOURNAL OF CLINICAL MICROBIOLOGY

The Microbial Engines That Drive Earth's Biogeochemical Cycles

(2008) P. G. Falkowski et al.   SCIENCE